Dear Reza Ganjalikhany,
You need to generate molecular fragment(s) from molecule(s)...
See
http://q4md-forcefieldtools.org/REDServer-Development/
To add phopshate groups to molecules see
http://q4md-forcefieldtools.org/REDDB/projects/F-90/
However your case is slightly different:
I load leaprc.ff99SB as an example in Amber12 and run the 'charge' command:
xleap -f leaprc.ff99SB
> charge DC
Total unperturbed charge: -1.000000
Total perturbed charge: -1.000000
> charge DC5
Total unperturbed charge: -0.307900
Total perturbed charge: -0.307900
> charge DC3
Total unperturbed charge: -0.692100
Total perturbed charge: -0.692100
As you can see the total charge of the fragments DC5 + DC3 = DC =
integer value
if you do want to put 'something' at the 5' position, it has to have a
total charge = -0.3079 (if you load leaprc.ff99SB)
now 'something' is, I guess, the three phosphate groups like in UTP as
shown in the Java applet at the RED Server Dev. home page:
http://q4md-forcefieldtools.org/REDServer-Development/mol2-Jmol/javaapplet7.html
You can find many examples of fragment generation at:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php
Your strategy to generate that/these fragments highly depends if you
want to add one and/or two and/or three and/or more phosphate groups
at 5'...
in your case you could use an intra-mcc on an alkyl group which would
cap these/that phosphate group(s)
See
http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#16
(but obviously here the constraint does not equal zero - see above)
See
http://q4md-forcefieldtools.org/REDServer-Development/
to prepare inputs:
http://q4md-forcefieldtools.org/Tutorial/Mini-HowTo-InputFiles.pdf
http://q4md-forcefieldtools.org/REDServer-Development/Documentation/
http://q4md-forcefieldtools.org/REDServer-Development/Documentation/Project.config
MOLECULE1-INTRA-MCC1 = -0.3079 | 1 2 3 4 | Remove
then look at the RRMS (should be close to zero) and r2 (should be
close to one) values of the fit with intra-mcc to check the impact of
that intra-mcc
(compare the fits without and with that intra-mcc)
regards, Francois
> I have already checked all the previous emails in the mailing list to find
> a standard procedure to safely parameterize three-phosphate-nucleotide at
> 5' end of a DNA molecule and all methods have been tested but non of them
> were helpful. There is a helpful email which is archived from 2006 but all
> the links were inactive and not operational.
> http://structbio.vanderbilt.edu/archives/amber-archive/2006/2341.php
>
> I would be grateful is any body could help me with this problem.
>
> On Fri, May 27, 2016 at 2:02 PM, M. Reza Ganjalikhany <
> ganjalikhany.gmail.com> wrote:
>
>> I used same names for mol2, Lib and PDB files but think that Leap does
>> not use my library.
>>
>> On Fri, May 27, 2016 at 12:55 PM, Vlad Cojocaru <
>> vlad.cojocaru.mpi-muenster.mpg.de> wrote:
>>
>>> The atom and residue names in your Leap library (mol2 or off library,
>>> don't know what you used) should exactly match the corresponding names
>>> in your complete PDB file ...otherwise it will not work because leap
>>> only knows what is in its template libraries ... So, playing with names
>>> will not help you, you have to match the names 100% to the Leap library
>>> ...
>>>
>>> Vlad
>>>
>>>
>>> On 05/27/2016 10:11 AM, M. Reza Ganjalikhany wrote:
>>> > Dear Amber Users,
>>> >
>>> > I want to simulate a DNA structure (DNAzyme) with a nick ( 5'
>>> > three-phosphate) inside the structure. I introduced a nick and add
>>> > three-phosphate to the Guanine, then I followed the standard procedure
>>> > with *antechamber
>>> > *to generate *library *and *frcmod * for this three-phosphate Guanine.
>>> > These file have been successfully generated and then I used these files
>>> > for generating parameter topology and input coordination for the whole
>>> > DNAzyme structure.
>>> > Unfortunately I got the " atoms not in residue templates" error from the
>>> > xleap for the P and O atoms.
>>> > I tried different name for phosphate and oxygen as below:
>>> > Alpha-beta-gamma phosphate
>>> > PA
>>> > O1A
>>> > O2A
>>> > PB
>>> > O1B
>>> > O2B
>>> > PG
>>> > O1G
>>> > O2G
>>> > O3G
>>> >
>>> > and also use plain P or O
>>> > P
>>> > OP1
>>> > OP2
>>> > ..
>>> > .
>>> >
>>> > but non of them helped me to solve the problem.
>>> > I used Hyperchem to add three-phosphate to Guanine residue, so I edited
>>> > these name according to standard names.
>>> > Is there any standard method for nomenclature of Phosphate and Oxygen
>>> > groups?
>>> > Should I use Chimera to generate there files or is there any procedure
>>> to
>>> > solve these phosphate-type-errors?
>>> >
>>> > Any help would be greatly appreciated.
>>> >
>>> > Regards,
>>> > M. Reza
F.-Y. Dupradeau
---
http://q4md-forcefieldtools.org/FyD/
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon May 30 2016 - 00:00:02 PDT
